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2.1.2.1: glycine hydroxymethyltransferase

This is an abbreviated version!
For detailed information about glycine hydroxymethyltransferase, go to the full flat file.

Word Map on EC 2.1.2.1

Reaction

5,10-methylenetetrahydrofolate
+
glycine
 +
H2O
=
tetrahydrofolate
 +
L-serine

Synonyms

AtSHMT3, bsSHMT, bstSHMT, EC 4.1.2.6, eSHMT, GlyA, GlyA protein, glycine hydroxymethyltransferrase, hSHMT, L-serine hydroxymethyltransferase, mitochondrial serine hydroxymethyltransferase, MJ1597, PvSHMT, Rhg4, serine hydroxymethyl transferase, serine hydroxymethylase hydroxymethyltransferase, serine, serine hydroxymethyltransferase, serine hydroxymethyltransferase 1, serine hydroxymethyltransferase 2, serine hydroxymethyltransferase 2alpha, serine transhydroxymethylase, serine:H4F hydroxymethyltransferase, serine:tetrahydrofolate hydroxymethyltransferase, SHM1, SHM2, SHMT, SHMT-1, SHMT-L, SHMT-S, SHMT08, SHMT1, SHMT2, SHMT2alpha, SHMT3, zcSHMT, zebrafish cytosolic serine hydroxymethyltransferase, zebrafish mitochondiral serine hydroxymethyltransferase, zmSHMT

ECTree

     2 Transferases
         2.1 Transferring one-carbon groups
             2.1.2 Hydroxymethyl-, formyl- and related transferases
                2.1.2.1 glycine hydroxymethyltransferase

Crystallization

Crystallization on EC 2.1.2.1 - glycine hydroxymethyltransferase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of K226M and K226Q mutant enzymes and of the complex of mutant enzyme K226Q with Gly or mutant enzyme K226M with Ser. Crystals are obtained by mixing 0.004 ml of protein solution 0.375 mM with 0.004 mM of reservoir solution containing 100 mM Hepes buffer, pH 7.5, 0.2 mM EDTA, 5 mM 2-mercaptoethanol, and 50% 2-methyl-2,4-pentanediol
-
crystals of Y51F and Y61A SHMT mutants are obtained by hanging drop vapour diffusion using 50% (v/v) 2-methyl 2,4-pentanediol as the precipitant
-
internal aldimine form, external aldimine form with bound serine and glycine, ternary complex with glycine and 5-formyl tetrahydrofolate
-
mutant proteins are crystallized by the hanging drop vapor diffusion method, using 50% 2-methyl 2,4-pentanediol as the precipitant with 0.2 mM EDTA, 5 mM beta-mercaptoethanol in 100 mM HEPES (pH 7.5)
hanging drop vapor diffusion method, using 20% (w/v) PEG 3350, 0.2 M sodium acetate
holo- and apo-isoform SHMT2, hanging drop vapor diffusion method, using 0.1 M Bis/Tris propane pH 7.5, 5% (v/v) glycerol, 12-16% (w/v) poly(ethylene glycol) 3350, 0.2 M potassium fluoride
mutant H135N/R137A/E168N, hanging drop vapor diffusion method, using 0.1 M sodium cacodylate pH 6.5, 1.0 M sodium citrate
sitting drop vapor diffusion method, using 0.1 M Bis-Tris pH 6.5, 28% (w/v) PEGMME 2000 (in complex with lometrexol and methotrexate), 0.2 M LiCl2, 0.1 M MES pH 6.0, 20% (w/v) PEG6000 (in complex with pemetrexed), and 0.2 M NaCl, 0.1 M MES pH 6.0, 20% (w/v) PEG6000 (in complex with raltitrexed)
hanging drop vapor diffusion method, using 18% (w/v) PEG 8000, 0.1 M MES pH 6.0, 0.2 M Ca(OAc)2
apoenzyme,hanging drop vapor diffusion method, using 55% tacsimate pH 7.0. Enzyme bound to reaction intermediates, hanging drop vapor diffusion method, using 75 mM MES pH 6.5, 19%(w/v) polyethylene glycol 3350 and 150 mMammonium acetate
crystal structure of the apoenzyme and pyridoxal 5'-phosphate-bound holoenzyme at 2.83 and 3.0 A resolution, respectively. The crystal structure of archaeal serine hydroxymethyltransferase reveals idiosyncratic features likely required to withstand high temperatures
crystal structure at 2.7 A resolution of the recombinant enzyme with active-site bound 5-formyl-tetrahydropteroylglutamate is obtained by soaking unliganded crystals of of the recombinant enzyme in 5-formyl-tetrahydropteroylglutamate, the conformation of the pteridine ring and its interactions with the enzyme differ slightly from those observed in complexes of the monoglutamate cofactor
-
hanging-drop vapour diffusion technique. Crystals of both mutants, E75L and E75Q are obtained by mixing 0.003v ml of an enzyme solution (34-44 mg/ml in 20 mM potassium phosphate, pH 7.3, with 1 mM dithiothreitol) with an equal volume of reservoir solution. The reservoir solution for E75L rcSHMT consists of 50 mM potassium phosphate, pH 6.6, 8.5-9.1% PEG 8000, and 100 mM KCl. For E75Q rcSHMT the reservoir solution consists of 15 mM potassium 2-(N-morpholino)ethanesulfonate, pH 6.4, 8.5-10% PEG 4000, and 30 mM KCl. Serine complexes are formed by adding 0.00025 ml of 250 mM L-serine directly to the drop
mitochondrial enzyme
-
in complex with inhibitor, microbatch method, using 20-24% (w/v) PEG 4000, 0.06-0.12 M NaCl, 0.1 M Tris-HCl buffer, pH 8.5, and 10% (v/v) trifluoroethanol
purified enzyme in a binary complex with L-serine and in a ternary complex with D-serine and (6R)-5-formyltetrahydrofolate, microbatch method, mixing of 0.001 ml of 0.38 mM protein in 0.86 mM PLP, 62 mM 2-mercaptoethanol, 87 mM Gly, L-Ser, or D-Ser, and 43 mM tetrahydrofolate, with 0.001 ml of well solution containing 20-21% w/v PEG 4000, 70-90 mM NaCl, 100 mM Tris-HCl, pH 8.5, 15% v/v trifluoroethanol, 20°C, 1-4 days, X-ray diffraction structure determination and analysis at 2.4-2.5 A resolution, molecular replacement
substrate binding structure analysis using crystal structure of the homodimeric PvSHMT in complex with D-serine and formyltetrahydrofolate, PDB ID 4OYT
-
purified recombinant enzyme in apoform, mixing of 200 nl of 10 mg/ml protein in 50 mM HEPES, pH 7.2, and 0.2 mM DTT with 200 nl of well solution containing 2M ammonium sulfate, 150 mM sodium chloride, and 100 mM sodium cacodylate, pH 6.5, 4°C, several days, X-ray diffraction structure determination and analysis at 1.85 A resolution, molecular replacement and modeling